Microbeads to Detect Matrix Deformations

This example calculates matrix deformations around a Human Umbilical Vein Endothelial Cells (HUVECs) that invades in a polyethylene glycol (PEG) hydrogel cell as measured and described in [Jorge Barrasa-Fano et al., 2021]. The data is available from the authors website here. Images of microbeads (channel ‘ch01’) between a relaxed and deformed stacks are used to calculate matrix deformations (image on the right).

import saenopy

Loading the Stacks

Saenopy is very flexible in loading stacks from any filename structure. We replace the number of the channels “ch00” with a channel placeholder “ch{c:01}” to indicate that this refers to the channels and which channel to use as the first channel where the deformations should be detected. We replace the number of the z slice “z000” with a z placeholder “z{z}” to indicate that this number refers to the z slice. We do the same for the deformed state and for the reference stack. Here images of microbeads (channel ‘ch01’) are used to calculate matrix deformation.

# load the relaxed and the contracted stack
# {z} is the placeholder for the z stack
# {c} is the placeholder for the channels
# {t} is the placeholder for the time points
results = saenopy.get_stacks(
    'TestDataTFMlabKULeuven\Stressed_z{z}_ch{c:01}.tif',
    reference_stack='TestDataTFMlabKULeuven\Relaxed_z{z}_ch{c:01}.tif',
    output_path='3_BeadMeasurement/example_output',
    voxel_size=[0.567, 0.567, 0.493])

Detecting the Deformations

Saenopy uses 3D Particle Image Velocimetry (PIV) with the following parameters to calculate matrix deformations between a deformed and relaxed state.

Piv Parameter	Value
element_size	5
window_size	25
signal_to_noise	1.1
drift_correction	True

# define the parameters for the piv deformation detection
piv_parameters = {'element_size': 5.0, 'window_size': 25.0, 'signal_to_noise': 1.1, 'drift_correction': True}


# iterate over all the results objects
for result in results:
    # set the parameters
    result.piv_parameters = piv_parameters
    # get count
    count = len(result.stacks)
    if result.stack_reference is None:
        count -= 1
    # iterate over all stack pairs
    for i in range(count):
        # get two consecutive stacks
        if result.stack_reference is None:
            stack1, stack2 = result.stacks[i], result.stacks[i + 1]
        # or reference stack and one from the list
        else:
            stack1, stack2 = result.stack_reference, result.stacks[i]
        # and calculate the displacement between them
        result.mesh_piv[i] = saenopy.get_displacements_from_stacks(stack1, stack2,
                                                                   piv_parameters["window_size"],
                                                                   piv_parameters["element_size"],
                                                                   piv_parameters["signal_to_noise"],
                                                                   piv_parameters["drift_correction"])
    # save the displacements
    result.save()